Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012114.1 Kokia drynarioides strain JFW-HI SEQ_127113, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 41174
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:390 original size:30 final size:30
Alignment explanation
Indices: 356--414 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
346 TTAAGGTTTC
356 CTTGCTTTTCTTATTGAAGAAGATGAATGT
1 CTTGCTTTTCTTATTGAAGAAGATGAATGT
386 CTTGCTTTTCTTATTGAAGAAGATGAATG
1 CTTGCTTTTCTTATTGAAGAAGATGAATG
415 AAAATCTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.42
Consensus pattern (30 bp):
CTTGCTTTTCTTATTGAAGAAGATGAATGT
Found at i:7430 original size:29 final size:29
Alignment explanation
Indices: 7370--7431 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
7360 CCTTGATTCT
* **
7370 CTTCTGTTGTAGTGGTTCCTTGATTTTTG
1 CTTCTGTTGAAGTGGTTCCTTGATTTACG
*
7399 CTTCTGTTGAAGTGTTTCCTTGATTTACG
1 CTTCTGTTGAAGTGGTTCCTTGATTTACG
7428 CTTC
1 CTTC
7432 CTGTAGCTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.10, C:0.18, G:0.21, T:0.52
Consensus pattern (29 bp):
CTTCTGTTGAAGTGGTTCCTTGATTTACG
Found at i:8908 original size:9 final size:10
Alignment explanation
Indices: 8884--8916 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
8874 AAGTAAAATT
8884 AAATTAATCA
1 AAATTAATCA
8894 AAATTAATC-
1 AAATTAATCA
*
8903 AAATTAATTA
1 AAATTAATCA
8913 AAAT
1 AAAT
8917 AAATATGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (10 bp):
AAATTAATCA
Found at i:9355 original size:42 final size:42
Alignment explanation
Indices: 9258--9358 Score: 166
Period size: 42 Copynumber: 2.4 Consensus size: 42
9248 TTAATGAATT
* *
9258 TAATATTTATCTAAATATTAATATGAGATATTAAATTAAATT
1 TAATATTTATCTAGATATTAATATGAGATATTAAATTAAATA
* *
9300 TAATGTTTATCTAGATATTAATATGAGATATTAAATTTAATA
1 TAATATTTATCTAGATATTAATATGAGATATTAAATTAAATA
9342 TAATATTTATCTAGATA
1 TAATATTTATCTAGATA
9359 ATATTTTATT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.46
Consensus pattern (42 bp):
TAATATTTATCTAGATATTAATATGAGATATTAAATTAAATA
Found at i:12915 original size:25 final size:25
Alignment explanation
Indices: 12886--12938 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
12876 GTTTAATTCC
12886 TTCTTGTAATTTAGG-TTTAGTTATT
1 TTCTT-TAATTTAGGTTTTAGTTATT
**
12911 TTCTTTTCTTTAGGTTTTAGTTATT
1 TTCTTTAATTTAGGTTTTAGTTATT
12936 TTC
1 TTC
12939 ATTCTTGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 7 0.28
25 18 0.72
ACGTcount: A:0.15, C:0.08, G:0.13, T:0.64
Consensus pattern (25 bp):
TTCTTTAATTTAGGTTTTAGTTATT
Found at i:12943 original size:24 final size:24
Alignment explanation
Indices: 12895--12944 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
12885 CTTCTTGTAA
*
12895 TTTAGGTTTAGTTATTTTCTTTTC
1 TTTAGGTTTAGTTATTTTCTATTC
12919 TTTAGGTTTTAGTTATTTTC-ATTC
1 TTTAGG-TTTAGTTATTTTCTATTC
12943 TT
1 TT
12945 GTTTTACGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.14, C:0.08, G:0.12, T:0.66
Consensus pattern (24 bp):
TTTAGGTTTAGTTATTTTCTATTC
Found at i:18000 original size:14 final size:15
Alignment explanation
Indices: 17965--18002 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
17955 ATTATTTTTA
17965 TATTGAATTTCGAAT
1 TATTGAATTTCGAAT
* *
17980 TAATGAATTT-TAAT
1 TATTGAATTTCGAAT
17994 TATTGAATT
1 TATTGAATT
18003 AAAAGTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 11 0.55
15 9 0.45
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.50
Consensus pattern (15 bp):
TATTGAATTTCGAAT
Found at i:24482 original size:25 final size:25
Alignment explanation
Indices: 24453--24505 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
24443 GTTTAACTCC
24453 TTCTTGTAATTTAGG-TTTAGTTATT
1 TTCTT-TAATTTAGGTTTTAGTTATT
**
24478 TTCTTTTCTTTAGGTTTTAGTTATT
1 TTCTTTAATTTAGGTTTTAGTTATT
24503 TTC
1 TTC
24506 ATTCTTGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 7 0.28
25 18 0.72
ACGTcount: A:0.15, C:0.08, G:0.13, T:0.64
Consensus pattern (25 bp):
TTCTTTAATTTAGGTTTTAGTTATT
Found at i:24510 original size:24 final size:24
Alignment explanation
Indices: 24462--24511 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
24452 CTTCTTGTAA
*
24462 TTTAGGTTTAGTTATTTTCTTTTC
1 TTTAGGTTTAGTTATTTTCTATTC
24486 TTTAGGTTTTAGTTATTTTC-ATTC
1 TTTAGG-TTTAGTTATTTTCTATTC
24510 TT
1 TT
24512 GTTTTATAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.14, C:0.08, G:0.12, T:0.66
Consensus pattern (24 bp):
TTTAGGTTTAGTTATTTTCTATTC
Found at i:25753 original size:21 final size:21
Alignment explanation
Indices: 25729--25771 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
25719 ATATTTGCCA
25729 ACAGATCATAAATAAGGTTTC
1 ACAGATCATAAATAAGGTTTC
* *
25750 ACAGATCATAGATGAGGTTTC
1 ACAGATCATAAATAAGGTTTC
25771 A
1 A
25772 AGTGAGAGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.28
Consensus pattern (21 bp):
ACAGATCATAAATAAGGTTTC
Found at i:26202 original size:66 final size:66
Alignment explanation
Indices: 26096--26222 Score: 254
Period size: 66 Copynumber: 1.9 Consensus size: 66
26086 CCCTTGGGTT
26096 CCCAGATTCAACTTTTTCCCCTAAAATCTGAAATGTTAAAGATAAGATGAATAAGAGGGCAGCGT
1 CCCAGATTCAACTTTTTCCCCTAAAATCTGAAATGTTAAAGATAAGATGAATAAGAGGGCAGCGT
26161 C
66 C
26162 CCCAGATTCAACTTTTTCCCCTAAAATCTGAAATGTTAAAGATAAGATGAATAAGAGGGCA
1 CCCAGATTCAACTTTTTCCCCTAAAATCTGAAATGTTAAAGATAAGATGAATAAGAGGGCA
26223 CCAAAAAGTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (66 bp):
CCCAGATTCAACTTTTTCCCCTAAAATCTGAAATGTTAAAGATAAGATGAATAAGAGGGCAGCGT
C
Found at i:29686 original size:21 final size:20
Alignment explanation
Indices: 29652--29696 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
29642 TTTAGTTCTT
29652 AATTTTTAAAATTT-AGTAAA
1 AATTTTTAAAATTTCA-TAAA
*
29672 AATTTTTAACGATTTCATAAA
1 AATTTTTAA-AATTTCATAAA
29693 AATT
1 AATT
29697 AAAATATCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 9 0.41
21 12 0.55
22 1 0.05
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.44
Consensus pattern (20 bp):
AATTTTTAAAATTTCATAAA
Found at i:34179 original size:20 final size:18
Alignment explanation
Indices: 34149--34200 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
34139 AATTTAATAC
34149 TTTTT-AATTTTATAATTT
1 TTTTTCAATTTTA-AATTT
*
34167 TTTTGTCAATTTTACATTT
1 TTTT-TCAATTTTAAATTT
*
34186 TTTTTCAGTTTTAAA
1 TTTTTCAATTTTAAA
34201 AGATTTTCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 13 0.45
19 9 0.31
20 7 0.24
ACGTcount: A:0.25, C:0.06, G:0.04, T:0.65
Consensus pattern (18 bp):
TTTTTCAATTTTAAATTT
Found at i:35276 original size:34 final size:34
Alignment explanation
Indices: 35233--35311 Score: 158
Period size: 34 Copynumber: 2.3 Consensus size: 34
35223 AATTTCTAAT
35233 TCAATCGATTCAACCTCTTTATTTGAACCTTATA
1 TCAATCGATTCAACCTCTTTATTTGAACCTTATA
35267 TCAATCGATTCAACCTCTTTATTTGAACCTTATA
1 TCAATCGATTCAACCTCTTTATTTGAACCTTATA
35301 TCAATCGATTC
1 TCAATCGATTC
35312 TTGGTCCAAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.29, C:0.24, G:0.06, T:0.41
Consensus pattern (34 bp):
TCAATCGATTCAACCTCTTTATTTGAACCTTATA
Found at i:35992 original size:16 final size:16
Alignment explanation
Indices: 35959--36001 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
35949 CAATCACTCC
** *
35959 CGTTATAACATTATTT
1 CGTTATAACAACAGTT
35975 CGTTATAACAACAGTT
1 CGTTATAACAACAGTT
*
35991 CGCTATAACAA
1 CGTTATAACAA
36002 TCAAGTTTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (16 bp):
CGTTATAACAACAGTT
Found at i:36694 original size:21 final size:21
Alignment explanation
Indices: 36670--36719 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
36660 ATTATCACTC
36670 TATAACAACATGTTATAAGAG
1 TATAACAACATGTTATAAGAG
36691 TATAACAACATGTTATAAGAG
1 TATAACAACATGTTATAAGAG
36712 TATAACAA
1 TATAACAA
36720 TCACCTCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.28
Consensus pattern (21 bp):
TATAACAACATGTTATAAGAG
Done.